ENST00000646572.2:n.230-1649T>C

Variant names:

• chr11-118702959-T-C
• rs574383
• ENST00000646572.2:n.230-1649T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646572.2(ENSG00000255422):​n.230-1649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,936 control chromosomes in the GnomAD database, including 9,133 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9133 hom., cov: 31)
• Consequence: ENSG00000255422 ENST00000646572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 8 publications found

Genes affected

ENSG00000255422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369519	XR_001748408.2	n.113-1649T>C		intron_variant	Intron 1 of 2
LOC105369519	XR_007062909.1	n.252-1649T>C		intron_variant	Intron 2 of 3
LOC105369519	XR_007062910.1	n.206-1649T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255422	ENST00000646572.2	n.230-1649T>C		intron_variant	Intron 1 of 2
ENSG00000255422	ENST00000702882.1	n.230-1720T>C		intron_variant	Intron 1 of 2
ENSG00000255422	ENST00000775653.1	n.230+2316T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51613 AN: 151818 Hom.: 9116 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.340 AC: 51676 AN: 151936 Hom.: 9133 Cov.: 31 AF XY: 0.339 AC XY: 25134 AN XY: 74244

African (AFR) AF: 0.350 AC: 14512 AN: 41448

American (AMR) AF: 0.473 AC: 7202 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1946 AN: 5162

South Asian (SAS) AF: 0.182 AC: 876 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3183 AN: 10534

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21549 AN: 67944

Other (OTH) AF: 0.345 AC: 726 AN: 2106

Alfa AF: 0.336 Hom.: 1110

Bravo AF: 0.360

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.80
PhyloP100		0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs574383; hg19: chr11-118573668;